Author details

Full Name

Lior Pachter

Affiliation

ORCID

Career Start Year

1999

Papers

159

H Index

Expertise

CM4AI Collaborator

PMID	Paper Title	Journal Title	Published Year
36660179	Length biases in single-cell RNA sequencing of pre-mRNA.		2023
38041403	New and notable: Revisiting the "two cultures" through extrinsic noise.		2023
37751736	Studying stochastic systems biology of the cell with single-cell genomics data.		2023
37673062	Direct androgen receptor control of sexually dimorphic gene expression in the mammalian kidney.	Dev Cell	2023
37601972	A standard for sharing spatial transcriptomics data.		2023
37745572	Universal preprocessing of single-cell genomics data.		2023
37745403	Biophysically Interpretable Inference of Cell Types from Multimodal Sequencing Data.		2023
37590228	The specious art of single-cell genomics.		2023
37828255	Assessing Markovian and Delay Models for Single-Nucleus RNA Sequencing.		2023
37684312	Author Correction: Principles of open source bioinstrumentation applied to the poseidon syringe pump system.		2023
36712140	Biophysical modeling with variational autoencoders for bimodal, single-cell RNA sequencing data.		2023
36711462	The telegraph process is not a subordinator.		2023
37205355	Direct androgen receptor regulation of sexually dimorphic gene expression in the mammalian kidney.	bioRxiv	2023
36993635	A machine-readable specification for genomics assays.		2023
36610997	Metadata retrieval from sequence databases with ffq.		2023
36610989	Efficient querying of genomic reference databases with gget.		2023
37051467	Cell-specific occupancy dynamics between the pioneer-like factor Opa/ZIC and Ocelliless/OTX regulate early head development in embryos.		2023
36993532	Flexible parsing, interpretation, and editing of technical sequences with splitcode.		2023
37292934	Studying stochastic systems biology of the cell with single-cell genomics data.		2023
37292896	The ENCODE4 long-read RNA-seq collection reveals distinct classes of transcript structure diversity.	bioRxiv	2023
37292888	Recovery of a learned behavior despite partial restoration of neuronal dynamics after chronic inactivation of inhibitory neurons.		2023
35132262	A Python library for probabilistic analysis of single-cell omics data.	Nat Biotechnol	2022
36094956	RNA velocity unraveled.	PLoS Computational Biology	2022
35440782	Publisher Correction: Museum of spatial transcriptomics.	Nature Methods	2022
36494337	Interpretable and tractable models of transcriptional noise for the rational design of single-molecule quantification experiments.		2022
35143775	Modeling bursty transcription and splicing with the chemical master equation.	Biophysical Journal	2022
34417615	SWALO: scaffolding with assembly likelihood optimization.	Nucleic Acids Research	2021
33795888	Modular, efficient and constant-memory single-cell RNA-seq preprocessing.	Nature Biotechnology	2021
33676365	Normalization of single-cell RNA-seq counts byâ¿¿log(x + 1)â¿ â¿¿orâ¿¿log(1 + x)â¿ .		2021
34211145	Massively scaled-up testing for SARS-CoV-2 RNA via next-generation sequencing of pooled and barcoded nasal and saliva samples.	Nat Biomed Eng	2021
34103073	BUTTERFLY: addressing the pooled amplification paradox with unique molecular identifiers in single-cell RNA-seq.		2021
34616073	Isoform cell-type specificity in the mouse primary motor cortex.	Nature	2021
34616066	A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex.	Nature	2021
34826233	Whole-animal multiplexed single-cell RNA-seq reveals transcriptional shifts across medusa cell types.	Science advances	2021
32942485	Special function methods for bursty models of transcription.	Physical Review E	2020
32070398	Protein velocity and acceleration from single-cell multiomics experiments.		2020
31873215	Highly multiplexed single-cell RNA-seq by DNA oligonucleotide tagging of cellular proteins.	Nat Biotechnol	2020
32484809	RefShannon: A genome-guided transcriptome assembler using sparse flow decomposition.	PLoS One	2020
33247933	A curated database reveals trends in single-cell transcriptomics.	Database : the journal of biological databases and curation	2020
32701060	Odd-paired is a pioneer-like factor that coordinates with Zelda to control gene expression in embryos.	eLife	2020
33303831	Reliable and accurate diagnostics from highly multiplexed sequencing assays.	Sci Rep	2020
30664774	A discriminative learning approach to differential expression analysis for single-cell RNA-seq.	Nature Methods	2019
31626771	Multimodal Analysis of Cell Types in a Hypothalamic Node Controlling Social Behavior.	Cell	2019
30654736	Barcode identification for single cell genomics.	BMC Bioinformatics	2019
31073610	The barcode, UMI, set format and BUStools.		2019
31162708	Factor analysis for survival time prediction with informative censoring and diverse covariates.	Statistics in Medicine	2019
30682053	Deterministic column subset selection for single-cell RNA-Seq.	PLoS ONE	2019
29650040	Gene-level differential analysis at transcript-level resolution.		2018
29967537	Accurate design of translational output by a neural network model of ribosome distribution.	Nature Structural and Molecular Biology	2018
30290149	RNA Velocity: Molecular Kinetics from Single-Cell RNA-Seq.	Molecular Cell	2018